BamQC report ----------------------------------- >>>>>>> Input bam file = SRR3084881.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP064210/SRP064210.result/quality.files/genome_results.txt >>>>>>> Reference number of bases = 3,095,693,983 bp number of contigs = 25 >>>>>>> Globals number of windows = 424 number of reads = 2,577,963 number of mapped reads = 2,275,583 (88.27%) number of supplementary alignments = 15,211 (0.59%) number of secondary alignments = 0 number of mapped bases = 158,358,226 bp number of sequenced bases = 158,295,613 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 102,301 duplication rate = 3.53% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 47.5105 >>>>>>> ACTG content number of A's = 46,384,100 bp (29.3%) number of C's = 29,110,370 bp (18.39%) number of T's = 50,603,036 bp (31.97%) number of G's = 32,173,263 bp (20.32%) number of N's = 24,844 bp (0.02%) GC percentage = 38.71% >>>>>>> Mismatches and indels general error rate = 0.0085 number of mismatches = 1,326,742 number of insertions = 12,702 mapped reads with insertion percentage = 0.55% number of deletions = 35,134 mapped reads with deletion percentage = 1.53% homopolymer indels = 48.54% >>>>>>> Coverage mean coverageData = 0.0512X std coverageData = 0.4675X There is a 4.27% of reference with a coverageData >= 1X There is a 0.63% of reference with a coverageData >= 2X There is a 0.1% of reference with a coverageData >= 3X There is a 0.02% of reference with a coverageData >= 4X There is a 0.01% of reference with a coverageData >= 5X There is a 0% of reference with a coverageData >= 6X There is a 0% of reference with a coverageData >= 7X There is a 0% of reference with a coverageData >= 8X There is a 0% of reference with a coverageData >= 9X There is a 0% of reference with a coverageData >= 10X There is a 0% of reference with a coverageData >= 11X There is a 0% of reference with a coverageData >= 12X There is a 0% of reference with a coverageData >= 13X There is a 0% of reference with a coverageData >= 14X There is a 0% of reference with a coverageData >= 15X There is a 0% of reference with a coverageData >= 16X There is a 0% of reference with a coverageData >= 17X There is a 0% of reference with a coverageData >= 18X There is a 0% of reference with a coverageData >= 19X There is a 0% of reference with a coverageData >= 20X There is a 0% of reference with a coverageData >= 21X There is a 0% of reference with a coverageData >= 22X There is a 0% of reference with a coverageData >= 23X There is a 0% of reference with a coverageData >= 24X There is a 0% of reference with a coverageData >= 25X There is a 0% of reference with a coverageData >= 26X There is a 0% of reference with a coverageData >= 27X There is a 0% of reference with a coverageData >= 28X There is a 0% of reference with a coverageData >= 29X There is a 0% of reference with a coverageData >= 30X There is a 0% of reference with a coverageData >= 31X There is a 0% of reference with a coverageData >= 32X There is a 0% of reference with a coverageData >= 33X There is a 0% of reference with a coverageData >= 34X There is a 0% of reference with a coverageData >= 35X There is a 0% of reference with a coverageData >= 36X There is a 0% of reference with a coverageData >= 37X There is a 0% of reference with a coverageData >= 38X There is a 0% of reference with a coverageData >= 39X There is a 0% of reference with a coverageData >= 40X There is a 0% of reference with a coverageData >= 41X There is a 0% of reference with a coverageData >= 42X There is a 0% of reference with a coverageData >= 43X There is a 0% of reference with a coverageData >= 44X There is a 0% of reference with a coverageData >= 45X There is a 0% of reference with a coverageData >= 46X There is a 0% of reference with a coverageData >= 47X There is a 0% of reference with a coverageData >= 48X There is a 0% of reference with a coverageData >= 49X There is a 0% of reference with a coverageData >= 50X There is a 0% of reference with a coverageData >= 51X >>>>>>> Coverage per contig chr1 249250621 11624446 0.04663758089493386 0.8960405974440162 chr2 243199373 16317652 0.06709578153394334 0.5352335267886928 chr3 198022430 12070952 0.060957498602557295 0.28448003293659874 chr4 191154276 9498654 0.049691035946274095 0.2598450623292625 chr5 180915260 8587755 0.047468383816821204 0.2611812183026144 chr6 171115067 9392351 0.054889094015315436 0.27751618718890797 chr7 159138663 9314874 0.05853306685126543 0.45808439799860945 chr8 146364022 8720139 0.05957843246477608 0.8655071155821997 chr9 141213431 9486719 0.06718000499541718 0.4839976005118025 chr10 135534747 5523171 0.04075095960447692 0.3103439513417786 chr11 135006516 6845677 0.05070627109583362 0.3249446767347313 chr12 133851895 6929889 0.05177281203228389 0.26853956424703623 chr13 115169878 4057749 0.03523272812705419 0.21210267137724273 chr14 107349540 3252650 0.030299617492538858 0.2357528081059111 chr15 102531392 3560880 0.03472965625981163 0.21254537560769715 chr16 90354753 2902078 0.03211870879664737 0.2566784173525544 chr17 81195210 4320233 0.053207978648001523 0.272552442967688 chr18 78077248 6474005 0.08291794557103242 0.8992633847772502 chr19 59128983 2780225 0.047019665465918806 0.5098240989409526 chr20 63025520 2918825 0.046311795602797086 0.2633650899549109 chr21 48129895 1450384 0.030134784212598013 0.22292792991607588 chr22 51304566 1089926 0.02124422999699481 0.1624800789635949 chrMT 16571 256831 15.498823245428762 8.215611044860431 chrX 155270560 10596176 0.06824330381754275 0.3278139455983546 chrY 59373566 385985 0.006500957008376421 0.20542101402018034